In order to accommodate vital military intelligence information, the Supreme Commander of the Army of the Southern Cross asks for volunteers to re-establish communications with an isolated space station.
On a routine patrol, Dana Sterling and Bowie Grant discover a plot by the Robotech Masters to excavate around the site of the final destruction of the SDF-1. Bowie is captured and it is up to Dana to affect his rescue.
After successfully shooting down the giant alien ship, a ro-con mission is called for. Once again Dana's group is volunteered for the dangerous mission. On the eve of this dangerous mission, the members of this courageous squad prepare for battle.
Dana's 15th Alpha Tactical Armoured Corps succeeds in breaching the hull of the fallen alien vessel. They proceed through the gigantic ship in the hope of discovering any information concerning this new threat.
Failing in their attempts at capturing the humans who entered their ship, the Robotech Masters plot to raid a nearby city and capture as many humans as they can in order to experiment and see if they should fear this minor group of creatures.
Dana Sterling tries to get the war with the Robotech Masters out of her mind by attending a concert with Bowie. She meets a singer who she finds interesting only to discover later that he is a spy working for the military police.
The Robotech Masters plan a strange deception by introducing Zor into the ranks of the 15th Tactical Squadron of the Army of the Southern Cross in the hope of getting some information regarding earth's knowledge of protoculture.
Zor, the Robotech Master's unsuspecting spy, is subjected to rigorous psychological tests to determine if he is human. Dana cannot allow him to go unchallenged for the destruction he has caused and plans a daring midnight raid on the hospital.
General Leonard is convinced that Zor can help his army get information regarding the Robotech Masters (whether he is human or not). He assigns Zor a commission in the 15th squad and places Dana Sterling in charge of his "rehabilitation.
General Leonard calls for an all out attack against the Robotech Masters forces in Earth orbit near the moon. The plan does not include the 15th Tactical Squad, which spends most of its time trying to help Zor regain his memory.
Things on earth are settling into a pleasant domestic routine while the Robotech Masters and their bioroid army fights for their very survival against the pressure of the Tactical Space Corps of the Army of the Southern Cross.
Louise Nichols, a member of Dana Sterling's squad, builds a Robotech device that is exploited by the Military Police into an offensive weapon system. The deception causes Louise to break down and attack her friends and fellow soldiers.
Trying to escape from the Robotech Masters, Dana and her friends discover many secrets concerning the true nature of the civilization living aboard the flagship of the Robotech Masters and the entire process of biogenetic engineering.
Outright rebellion becomes the first order of the day, as Musica and Zor reject the teachings of the Robotech Masters and turn to aid the human captives. It is a fantastic journey in ultimate truths for Zor, as his originator's memory comes back to haunt him.
Musica tries to assimilate herself into the "alien" environment she finds on earth. Her joy of discovery in this nNova tracks Bowie and Musica to the crash site of the SDF-1 and makes a startling discovery in regard to the nature of Protoculture.
Nova tracks Bowie and Musica to the crash site of the SDF-1 and makes a startling discovery in regard to the nature of Protoculture and the growing threat of the impending Invid invasion. Zor realizes that the Robotech Masters must be stopped at any cost.
Zor and the rest of Dana Sterling's 15th Tactical Squad make a daring trip to the Robotech Masters' flagship in order to rescue General Rolf Emerson, Bowie's guardian, and try and put a stop to the second Robotech Wars.
The final battle of the Second Robotech War is fought as Zor goes on the rampage to destroy the entire culture created by the Robotech Masters before the arrival of the Invid. His plan fails, causing his destruction.